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DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems

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A second paradigm for gene activation in bacteria.

M Buck¹, D Bose, P Burrows

¹Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK. m.buck@imperial.ac.uk

Biochemical Society Transactions

|November 1, 2006

Summary

Bacterial enhancer binding proteins (EBPs) use ATP hydrolysis to open DNA, initiating gene transcription. This process involves a molecular switch in EBPs and the sigma(54) factor to activate RNA polymerase.

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Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

Gene expression control is crucial for cellular development and adaptation.
Bacterial enhancer binding proteins (EBPs) are key regulators of transcription initiation.
AAA(+) proteins utilize ATP hydrolysis for various cellular activities, including DNA remodeling.

Purpose of the Study:

To elucidate the mechanism of DNA template access during bacterial gene transcription.
To describe how ATP hydrolysis by transcriptional activators leads to DNA opening and transcription.
To detail the role of EBPs and the sigma(54) factor in promoter complex remodeling.

Main Methods:

Integrative structural and functional studies using purified bacterial transcription components.
Analysis of ATP hydrolysis-driven conformational changes in EBPs.
Investigating the interaction between EBPs, RNA polymerase (RNAP) holoenzyme, and the sigma(54) factor.

Main Results:

A specialized molecular machinery involving EBPs and ATP hydrolysis was identified for DNA opening.
A molecular switch in the EBP PspF controls the exposure of a loop that engages the RNAP promoter complex.
The sigma(54) factor mediates conformational changes in RNAP to form the open promoter complex.

Conclusions:

ATP hydrolysis by EBPs is essential for initiating DNA opening and transcription.
The EBP-sigma(54)-RNAP interaction is a critical regulatory step in gene expression.
This study provides a detailed mechanistic description of transcription initiation in bacteria.